This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot.

Related tags

Data AnalysissuperSFS
Overview

superSFS

This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot. It is easy-to-use and runing fast. What you should prepare is the phased vcf file containg the data of populations you intrested and the outgroup, the outgroup name file, and the annotation file. Enjoy it!!!

It has four models:

0:Using all function, from original vcf data to sfs barplot
1: Only speculate the ancestral allel and output new vcf file using speculated allel as reference
2: Only count the frequency of derived allel in each snp of each population
3: Only draw bar polt of sfs using data generated from the results of calutation of sfs

Example:

Model 0: python superSFS 0 ogdir threshold vcfdir annodir modir coutdir plotdir group
Model 1: python superSFS 1 ogdir threshold vcfdir outdir
Model 2: python superSFS 2 annodir modir coutdir
Model 3: python superSFS 3 coutdir plotdir group

Explation for each parameter:

ogdir: direction of outgroup names file
threshold: a number that if the sum of variant allel in outpgroup greater than it,the variant allel will be counted as ancestral allel
vcfdir: direction of vcf data
vannodir: direction of annotation file with sample names in first column and group name in second colum. This file should has header in first row
vmodir: assign the output direction of generated vcf file using speculated allel as reference
countdir: assign the output direction of calculation of derived allels for each snp in each group
plotdir: assign the output direction of bar plot of sfs
group: the group that you want to analysis
Pandas on AWS - Easy integration with Athena, Glue, Redshift, Timestream, QuickSight, Chime, CloudWatchLogs, DynamoDB, EMR, SecretManager, PostgreSQL, MySQL, SQLServer and S3 (Parquet, CSV, JSON and EXCEL).

AWS Data Wrangler Pandas on AWS Easy integration with Athena, Glue, Redshift, Timestream, QuickSight, Chime, CloudWatchLogs, DynamoDB, EMR, SecretMana

Amazon Web Services - Labs 3.3k Jan 04, 2023
Creating a statistical model to predict 10 year treasury yields

Predicting 10-Year Treasury Yields Intitially, I wanted to see if the volatility in the stock market, represented by the VIX index (data source), had

10 Oct 27, 2021
Vectorizers for a range of different data types

Vectorizers for a range of different data types

Tutte Institute for Mathematics and Computing 69 Dec 29, 2022
Bearsql allows you to query pandas dataframe with sql syntax.

Bearsql adds sql syntax on pandas dataframe. It uses duckdb to speedup the pandas processing and as the sql engine

14 Jun 22, 2022
Using Python to scrape some basic player information from www.premierleague.com and then use Pandas to analyse said data.

PremiershipPlayerAnalysis Using Python to scrape some basic player information from www.premierleague.com and then use Pandas to analyse said data. No

5 Sep 06, 2021
First and foremost, we want dbt documentation to retain a DRY principle. Every time we repeat ourselves, we waste our time. Second, we want to understand column level lineage and automate impact analysis.

dbt-osmosis First and foremost, we want dbt documentation to retain a DRY principle. Every time we repeat ourselves, we waste our time. Second, we wan

Alexander Butler 150 Jan 06, 2023
track your GitHub statistics

GitHub-Stalker track your github statistics 👀 features find new followers or unfollowers find who got a star on your project or remove stars find who

Bahadır Araz 34 Nov 18, 2022
PyChemia, Python Framework for Materials Discovery and Design

PyChemia, Python Framework for Materials Discovery and Design PyChemia is an open-source Python Library for materials structural search. The purpose o

Materials Discovery Group 61 Oct 02, 2022
Show you how to integrate Zeppelin with Airflow

Introduction This repository is to show you how to integrate Zeppelin with Airflow. The philosophy behind the ingtegration is to make the transition f

Jeff Zhang 11 Dec 30, 2022
Single-Cell Analysis in Python. Scales to >1M cells.

Scanpy – Single-Cell Analysis in Python Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It inc

Theis Lab 1.4k Jan 05, 2023
PCAfold is an open-source Python library for generating, analyzing and improving low-dimensional manifolds obtained via Principal Component Analysis (PCA).

PCAfold is an open-source Python library for generating, analyzing and improving low-dimensional manifolds obtained via Principal Component Analysis (PCA).

Burn Research 4 Oct 13, 2022
Elasticsearch tool for easily collecting and batch inserting Python data and pandas DataFrames

ElasticBatch Elasticsearch buffer for collecting and batch inserting Python data and pandas DataFrames Overview ElasticBatch makes it easy to efficien

Dan Kaslovsky 21 Mar 16, 2022
Statistical & Probabilistic Analysis of Store Sales, University Survey, & Manufacturing data

Statistical_Modelling Statistical & Probabilistic Analysis of Store Sales, University Survey, & Manufacturing data Statistical Methods for Decision Ma

Avnika Mehta 1 Jan 27, 2022
An extension to pandas dataframes describe function.

pandas_summary An extension to pandas dataframes describe function. The module contains DataFrameSummary object that extend describe() with: propertie

Mourad 450 Dec 30, 2022
Functional tensors for probabilistic programming

Funsor Funsor is a tensor-like library for functions and distributions. See Functional tensors for probabilistic programming for a system description.

208 Dec 29, 2022
MeSH2Matrix - A set of Python codes for the generation of biomedical ontologies from the MeSH keywords of the PubMed scholarly publications

A set of Python codes for the generation of biomedical ontologies from the MeSH keywords of the PubMed scholarly publications

SisonkeBiotik 6 Nov 30, 2022
Python-based Space Physics Environment Data Analysis Software

pySPEDAS pySPEDAS is an implementation of the SPEDAS framework for Python. The Space Physics Environment Data Analysis Software (SPEDAS) framework is

SPEDAS 98 Dec 22, 2022
A tool to compare differences between dataframes and create a differences report in Excel

similarpanda A module to check for differences between pandas Dataframes, and generate a report in Excel format. This is helpful in a workplace settin

Andre Pretorius 9 Sep 15, 2022
Monitor the stability of a pandas or spark dataframe ⚙︎

Population Shift Monitoring popmon is a package that allows one to check the stability of a dataset. popmon works with both pandas and spark datasets.

ING Bank 403 Dec 07, 2022
Automatic earthquake catalog building workflow: EQTransformer + Siamese EQTransformer + PickNet + REAL + HypoInverse

Automatic regional-scale earthquake catalog building workflow: EQTransformer + Siamese EQTransforme

Xiao Zhuowei 9 Nov 27, 2022